Analysis of PTMs in their structural context using the StructureMap and AlphaMap Python packages

This notebook contains the analyses presented in our [recent preprint](https://www.biorxiv.org/content/10.1101/2022.02.23.481596v1).

Prepare the environment

Download AlphaFold data

Note: The pae_dir and cif_dir locations need to be adjusted.

Format AlphaFold data

Annotate amino acid exposure metric

Full sphere exposure

Half sphere exposure

Smooth scores for unstructured regions

Annotate IDRs >> IDR_benchmark notebook

Visualize pPAE cutoff

Find short unstructured regions within large folded domains

David enrichment analysis of GO MF

DAVID platform version 6.8

Kinase loop annotation

Here we read kinase substructures annotated in KinaseMD.

https://bioinfo.uth.edu/kmd/

Annotate PTM data

Assess kinase annotations

Kinases with structural annotation that have an alphafold structure

Gloops

Calpha-Helix

Aloops

Get list of all PTMs in short IDRs

Get list of all short IDRs

Visualization of short IDRs, activation loops and phosphosites

Get hotlist of PTMs in short IDRs

Find interesting Ubi in shrt IDR

Generate PTM site dict

Perform enrichment analysis

Enrichment results for Ishihama

Per protein enrichment

Ubiquitin

Enrichment of functional sites in short IDRs

Kinase motifs

Get kinase substrates

Proximity analysis

Evaluate PTM co-localization

3D PTM clusters

Cluster phosphosites in the covid dataset

Number of modifications from PSP

3D visualization with AlphaMap